Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

Handle URI:
http://hdl.handle.net/10754/550142
Title:
Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region
Authors:
Arif, Chatchanit ( 0000-0001-5640-9970 ) ; Daniels, Camille; Bayer, Till; Banguera Hinestroza, Eulalia; Barbrook, Adrian; Howe, Christopher J.; LaJeunesse, Todd C.; Voolstra, Christian R. ( 0000-0003-4555-3795 )
Abstract:
The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region 2014, 23 (17):4418 Molecular Ecology
Publisher:
Wiley
Journal:
Molecular Ecology
Issue Date:
Sep-2014
DOI:
10.1111/mec.12869
PubMed ID:
25052021
PubMed Central ID:
PMC4285332
Type:
Article
ISSN:
09621083
Additional Links:
http://doi.wiley.com/10.1111/mec.12869
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorArif, Chatchaniten
dc.contributor.authorDaniels, Camilleen
dc.contributor.authorBayer, Tillen
dc.contributor.authorBanguera Hinestroza, Eulaliaen
dc.contributor.authorBarbrook, Adrianen
dc.contributor.authorHowe, Christopher J.en
dc.contributor.authorLaJeunesse, Todd C.en
dc.contributor.authorVoolstra, Christian R.en
dc.date.accessioned2015-04-15T14:05:35Zen
dc.date.available2015-04-15T14:05:35Zen
dc.date.issued2014-09en
dc.identifier.citationAssessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region 2014, 23 (17):4418 Molecular Ecologyen
dc.identifier.issn09621083en
dc.identifier.pmid25052021en
dc.identifier.doi10.1111/mec.12869en
dc.identifier.urihttp://hdl.handle.net/10754/550142en
dc.description.abstractThe persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.en
dc.publisherWileyen
dc.relation.urlhttp://doi.wiley.com/10.1111/mec.12869en
dc.rightsThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.en
dc.subjectcoral reefsen
dc.subjectdinoflagellatesen
dc.subjectinternal transcribed spacer 2en
dc.subjectnext-generation sequencingen
dc.subjectoperational taxonomic uniten
dc.subjectSymbiodiniumen
dc.titleAssessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA regionen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalMolecular Ecologyen
dc.identifier.pmcidPMC4285332en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionGEOMAR Helmholtz Centre for Ocean Research Kiel; 24105 Kiel Germanyen
dc.contributor.institutionDepartment of Biochemistry; University of Cambridge; Building O Downing Site Tennis Court Road Cambridge CB2 1QW UKen
dc.contributor.institutionDepartment of Biochemistry; University of Cambridge; Building O Downing Site Tennis Court Road Cambridge CB2 1QW UKen
dc.contributor.institutionDepartment of Biology; Penn State University; University Park PA 16802 USAen
kaust.authorArif, Chatchaniten
kaust.authorDaniels, Camille Arianen
kaust.authorVoolstra, Christian R.en
kaust.authorBanguera Hinestroza, Eulaliaen

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